CommunityData:Klone

Klone is the latest version of hyak, the UW super computing system. We will soon have a larger allocation of machines on Klone than on Mox. The Klone machines have 40 cores and either 384GB or 768GB of RAM.

Setup

The recommended way to manage software for your research projects on Klone is to use Singularity containers. You can build a singularity container on your local machine using the linux package manager of your choice. The instructions on this page document how to build the cdsc_base.sif singularity package which provides python, R, julia, and pyspark based on Debian 10 (Buster).

Installing singularity on your local computer

We want singularity version 3.7.1 which is the version installed oh klone. Follow these instructions for installing singularity on your local linux machine.

Creating a singularity container

On your local machine, run

sudo singularity build cdsc_base library://library/default/debian:10

This will create a new container called cdsc_base with a minimal installation of Debian Buster.

Next, we need to set aside some disk space where the container can install files.

Initial .Bashrc

Before we get started using our singularity package on klone, we need to start with a .bashrc that just sets the umask so that other members of the group can edit your files and that loads singularity.

# .bashrc
# Stuff that's in there already that you need for working with the cluster.
# Add the following two lines
umask 007
module load singularity/3.7.1
## this makes it so singularity can see /gscratch/comdata
export SINGULARITY_BIND="/gscratch/comdata:/gscratch/comdata"